1 Load the packages

suppressPackageStartupMessages({
library(knitr)
library(pander)
library(dygraphs)
library(zoo)
library(Quandl)
library(ggplot2)
library(rbokeh)
})

2 R Markdown Layout

3 Global settings

Before writing your RMarkdown document, user can specify the global settings for the global environment. For example, setting whether to echo your R code and show the code/results etc. in the document. You can either set the options globally or for individual code blocks.

## global setting for all blocks

{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE)

## setting for individual code block

{r chuck_name, echo = FALSE, results = "hide", include = TRUE}
x <- rnorm(100)
y <- 2*x + rnorm(100)

If you want all the figures take the same amount of space, use the following commands:

{r global_options, include = FALSE}
knitr::opts_chunk$set(fig.width = 12, fig.height = 8, fig.path = 'Figs/',
                      echo = FALSE, warning = FALSE, message = FALSE)
# While setting figure path, the '/' is very import.

Also, you can individually change the settings for your figure windows. This will overwrite global settings. This is very convenient especially when you have images for different data size. For example, by specifying ‘fig.with’ and ‘fig.height’:

{r scatterplot, fig.width = 8, fig.height = 6}
plot(x,y)

4 Create Paragraphs With Styles

4.1 Headers

# Header 1
## Header 2
### Header 3

4.2 Lists

4.2.1 Unordered List

* Item 1
* Item 2
    + Item 2a
    + Item 2b

This is the example output for Unordered Lists:

Item 1
ITem 2
- Item 2a
- Item 2b

4.2.2 Ordered List

1. Item 1
2. Item 2
3. Item 3
    + Item 3a
    + Item 3b

This is the example output for ordered list:

Item 1
Item 2
Item 3
- Item 3a
- Item 3b

4.3 Emphasis

From time to time, we might want to emphasize our text either using {**bold**} or {*italic*}. Also, we can change the text color by using styles. We can say roses are red, violets are blue by using command <span style="color:red">red</span> and <span style="color:blue">blue</span> repsectively.

5 Embed code chunk, inline code and run R code

5.1 R Code Chunks

R code will be evaluated and printed

size = 750
x = as.data.frame(matrix(runif(14*size),ncol=14))
head(x)

<<<<<<< HEAD

##          V1        V2         V3        V4          V5        V6
## 1 0.7548207 0.2945704 0.18991178 0.2991356 0.542085034 0.8699078
## 2 0.1722386 0.5325214 0.94117480 0.5981589 0.662857883 0.1253510
## 3 0.7185763 0.8012025 0.73345663 0.2198048 0.005043637 0.8216537
## 4 0.7281209 0.7730873 0.30950364 0.2475588 0.848580285 0.5912194
## 5 0.2927274 0.1946505 0.77037892 0.4902956 0.053748523 0.2242255
## 6 0.5568808 0.8588699 0.08851095 0.6293152 0.338115964 0.5248185
##           V7        V8        V9       V10       V11         V12       V13
## 1 0.96531414 0.6556900 0.4929799 0.4784724 0.9426973 0.003610311 0.2207848
## 2 0.32736569 0.3022840 0.4003558 0.3493958 0.2649559 0.746046715 0.8595444
## 3 0.77310659 0.8038141 0.9043817 0.2590332 0.6863734 0.125399736 0.2097843
## 4 0.09626997 0.3580368 0.3071267 0.7322447 0.2279688 0.877367509 0.2435542
## 5 0.42387970 0.5898082 0.7616771 0.6864669 0.9713130 0.340537479 0.7655595
## 6 0.81067242 0.3470121 0.6863067 0.7027534 0.7429288 0.272852706 0.2010344
##         V14
## 1 0.4627359
## 2 0.8190717
## 3 0.8079272
## 4 0.2574419
## 5 0.3926048
## 6 0.1062768

=======

##           V1        V2        V3         V4         V5          V6
## 1 0.33166033 0.1420655 0.2836498 0.75891100 0.31424165 0.697032094
## 2 0.82259151 0.9626836 0.2126412 0.15594293 0.96962867 0.627802575
## 3 0.78307095 0.4538515 0.6035929 0.63552651 0.87709911 0.094951871
## 4 0.61278501 0.2380527 0.2902754 0.04142245 0.33188859 0.389424942
## 5 0.43043430 0.8465630 0.6015905 0.06995226 0.89579034 0.334250760
## 6 0.01801764 0.6452595 0.5422810 0.36754360 0.07109973 0.005243477
##            V7        V8        V9       V10       V11        V12       V13
## 1 0.367260975 0.3372149 0.2330494 0.1844045 0.2548702 0.13115498 0.0783551
## 2 0.315287754 0.3600626 0.7621619 0.3251440 0.9335521 0.56685419 0.9037180
## 3 0.105956119 0.9608078 0.6674662 0.7091772 0.8803608 0.63756200 0.4141541
## 4 0.726666056 0.1358177 0.8948132 0.9952181 0.8469392 0.07849199 0.7698287
## 5 0.006574286 0.6294320 0.5281297 0.1160245 0.6145946 0.64806517 0.9942196
## 6 0.338450101 0.9253563 0.1131822 0.1603369 0.8691608 0.50156408 0.4531857
##         V14
## 1 0.5576812
## 2 0.6232648
## 3 0.7716351
## 4 0.2396432
## 5 0.4220654
## 6 0.8644235

>>>>>>> eb7e9f72e21ae9be1ba844417fccd9e82db6b18d

5.2 Embed Code Chunk

In RMarkdown, we can symply embed a chunk of code by using

x = matrix(runif(14*size),ncol=14)
y = 10 * sin(pi*x[,1]*x[,2]) + 20*(x[,3]-0.5)**2 + 10*x[,4] + 5*x[,5] + runif(1,0,1)
x[,11:14] = x[,1:4] + matrix(runif(4*size,min = 0, max = 0.025),ncol=4)

5.3 Inline Code

Inline code can be excecuted using two plus two equals 4 using two plus two equals 4

6 Generate R Graphics and Table

data=data.frame(value=rnorm(10000))
# Basic histogram
ggplot(data, aes(x=value)) + geom_histogram()

## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

<<<<<<< HEAD

# Custom Binning. I can just give the size of the bin
ggplot(data, aes(x=value)) + geom_histogram(binwidth = 0.05)

# Uniform color
ggplot(data, aes(x=value)) + 
    geom_histogram(binwidth = 0.2, color="white", fill=rgb(0.2,0.7,0.1,0.4) )

# Proportional color
ggplot(data, aes(x=value)) + 
    geom_histogram(binwidth = 0.2, aes(fill = ..count..) )

=======

# Custom Binning. I can just give the size of the bin
ggplot(data, aes(x=value)) + geom_histogram(binwidth = 0.05)

# Uniform color
ggplot(data, aes(x=value)) + 
    geom_histogram(binwidth = 0.2, color="white", fill=rgb(0.2,0.7,0.1,0.4) )

# Proportional color
ggplot(data, aes(x=value)) + 
    geom_histogram(binwidth = 0.2, aes(fill = ..count..) )

>>>>>>> eb7e9f72e21ae9be1ba844417fccd9e82db6b18d

7 Embed images, hyperlink, and advanced items (animation, interactive maps etc.)

Images on the web or local files in the same directory:

![](http://example.com/logo.png)
![optional caption text](figures/img.png)

IHS Markit

8 Embed Mathematic Equations

There are two ways to embed equations using LaTex format: inline equation and block equations.

8.1 Inline Equation

This is an example of inline equation using $ quotes. $10sin(\pi x_1x_2)$ ==> $10sin(\pi x_1x_2)$

8.2 Display Equations

This is an example of display equations using $$ quotes. $$y = 10sin(\pi x_1x_2) + 20(x_3-0.5)^2 + 10x_4+5x_5+\epsilon$$=> \[y = 10sin(\pi x_1x_2) + 20(x_3-0.5)^2 + 10x_4+5x_5+\epsilon\]

9 Tables

R Markdown can also create simple tables very easily by following syntax:

First Header | Second Header
------------ | -------------
Content Cell | Content Cell
Content Cell | Content Cell
Content Cell | Content Cell
Reference Style Links and Images

Here is an example output:

Name	Age	Hobby
Jack	22	Travel
Adam	33	Movie
Judy	25	Party

10 Auto Cite References

In RMarkdown, we can also easily cite our references by coupling with reference managers. For example: Application written in the R programming language [@RCoreTeam] using the Shiny framework [@Tutorialspoint2015].

11 Advanced Features

RMarkdown can also embed advanced objects into its HTML output: video, interactive graphics etc. Here are some examples of the advanced features:

11.1 Interactive graphs

11.1.1 Interactive time series

brent <- Quandl("EIA/PET_RBRTE_D", collapse="monthly", type="ts")
dygraph(brent, main = "Brent Spot Prices") %>% dyRangeSelector() %>% 
  dyAxis("y", label = "US $/Barrel") %>%
  dySeries("V1", label = "Brent ($/Barrel)") %>%
  dyLegend(show = "follow")

<<<<<<< HEAD ======= >>>>>>> eb7e9f72e21ae9be1ba844417fccd9e82db6b18d

11.1.2 GeoSpatial Visualization

library(leaflet)
m <- leaflet() %>%
  addTiles() %>%  # Add default OpenStreetMap map tiles
  addMarkers(lng=-77.003, lat=38.9, popup="IHS MARKIT")
m  # Print the map

<<<<<<< HEAD ======= >>>>>>> eb7e9f72e21ae9be1ba844417fccd9e82db6b18d

11.1.3 rbokeh

library(rbokeh)
figure() %>%
  ly_points(Sepal.Length, Sepal.Width, data = iris,
    color = Species, glyph = Species,
    hover = list(Sepal.Length, Sepal.Width))

<<<<<<< HEAD

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

## Warning in structure(x, class = unique(c("AsIs", oldClass(x)))): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
##   Consider 'structure(list(), *)' instead.

======= >>>>>>> eb7e9f72e21ae9be1ba844417fccd9e82db6b18d

11.1.4 networkViz

library(visNetwork)
nodes <- data.frame(id = 1:6, title = paste("node", 1:6), 
                    shape = c("dot", "square"),
                    size = 10:15, color = c("blue", "red"))
edges <- data.frame(from = 1:5, to = c(5, 4, 6, 3, 3))
visNetwork(nodes, edges) %>%
  visOptions(highlightNearest = TRUE, nodesIdSelection = TRUE)

<<<<<<< HEAD ======= >>>>>>> eb7e9f72e21ae9be1ba844417fccd9e82db6b18d

11.1.5 plotly

library(ggplot2)
library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

p <- ggplot(data = diamonds, aes(x = cut, fill = clarity)) +
            geom_bar(position = "dodge")
ggplotly(p)

## We recommend that you use the dev version of ggplot2 with `ggplotly()`
## Install it with: `devtools::install_github('hadley/ggplot2')`

<<<<<<< HEAD ======= >>>>>>> eb7e9f72e21ae9be1ba844417fccd9e82db6b18d

11.1.6 networkD3

# Load data
library(networkD3)

## 
## Attaching package: 'networkD3'

## The following object is masked from 'package:leaflet':
## 
##     JS

data(MisLinks)
data(MisNodes)

# Plot
forceNetwork(Links = MisLinks, Nodes = MisNodes,
            Source = "source", Target = "target",
            Value = "value", NodeID = "name",
            Group = "group", opacity = 0.8)

<<<<<<< HEAD ======= >>>>>>> eb7e9f72e21ae9be1ba844417fccd9e82db6b18d

URL <- paste0(
        "https://cdn.rawgit.com/christophergandrud/networkD3/",
        "master/JSONdata//flare.json")

## Convert to list format
Flare <- jsonlite::fromJSON(URL, simplifyDataFrame = FALSE)

# Use subset of data for more readable diagram
Flare$children = Flare$children[1:3]

radialNetwork(List = Flare, fontSize = 10, opacity = 0.9)

<<<<<<< HEAD

diagonalNetwork(List = Flare, fontSize = 10, opacity = 0.9)

hc <- hclust(dist(USArrests), "ave")

dendroNetwork(hc, height = 600)

=======

diagonalNetwork(List = Flare, fontSize = 10, opacity = 0.9)

hc <- hclust(dist(USArrests), "ave")

dendroNetwork(hc, height = 600)

>>>>>>> eb7e9f72e21ae9be1ba844417fccd9e82db6b18d

11.2 Video

#htmltools::includeHTML("embed_video_Rmarkdown.html")

<<<<<<< HEAD =======

REFERENCES

R Core Team. 2016. “R: A Language and Envirnoment for Statistical Computing.” Journal Article. http:///www.R-project.org.

Tutorialspoint. 2015. “Perl Programming.”

>>>>>>> eb7e9f72e21ae9be1ba844417fccd9e82db6b18d

RMarkdownDemo

liang kuang

2017-06-27

2017-06-15

1 Load the packages

2 R Markdown Layout

3 Global settings

4 Create Paragraphs With Styles

4.1 Headers

4.2 Lists

4.2.1 Unordered List

4.2.2 Ordered List

4.3 Emphasis

5 Embed code chunk, inline code and run R code

5.1 R Code Chunks

5.2 Embed Code Chunk

5.3 Inline Code

6 Generate R Graphics and Table

7 Embed images, hyperlink, and advanced items (animation, interactive maps etc.)

8 Embed Mathematic Equations

8.1 Inline Equation

8.2 Display Equations

9 Tables

10 Auto Cite References

11 Advanced Features

11.1 Interactive graphs

11.1.1 Interactive time series

11.1.2 GeoSpatial Visualization

11.1.3 rbokeh

11.1.4 networkViz

11.1.5 plotly

11.1.6 networkD3

11.2 Video

REFERENCES

12 REFERENCES